Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011261.1 Corchorus capsularis cultivar CVL-1 contig11282, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:763 original size:30 final size:31
Alignment explanation
Indices: 728--812 Score: 131
Period size: 30 Copynumber: 2.8 Consensus size: 31
718 ATAGGAATAG
*
728 TGATGCGCCCAA-GGTTTATCATGGAAGGAA
1 TGATGCGCCCAATGGCTTATCATGGAAGGAA
758 TGATGCG-CCAATGGCTTATCATGGAAGGAA
1 TGATGCGCCCAATGGCTTATCATGGAAGGAA
*
788 TGATGCG-CCAATGGCTTATTATGGA
1 TGATGCGCCCAATGGCTTATCATGGA
813 CTTGAAGACA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 4 0.08
30 48 0.92
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.26
Consensus pattern (31 bp):
TGATGCGCCCAATGGCTTATCATGGAAGGAA
Found at i:3083 original size:2 final size:2
Alignment explanation
Indices: 3040--3066 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3030 ATACGTAATT
3040 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3067 TTAAATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4758 original size:12 final size:12
Alignment explanation
Indices: 4741--4770 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4731 AAAAAGATAT
4741 CTATACTTATAC
1 CTATACTTATAC
*
4753 CTATACTTATAT
1 CTATACTTATAC
4765 CTATAC
1 CTATAC
4771 CTTTGGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (12 bp):
CTATACTTATAC
Found at i:9240 original size:2 final size:2
Alignment explanation
Indices: 9233--9263 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9223 TGCATTAATT
9233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9264 TTGAGGTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10740 original size:2 final size:2
Alignment explanation
Indices: 10723--10760 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
10713 ATATTTAGGC
10723 AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10761 AGAGAATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:10752 original size:19 final size:18
Alignment explanation
Indices: 10723--10760 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
10713 ATATTTAGGC
10723 ATATAATATAATATATAT
1 ATATAATATAATATATAT
10741 ATATATATATAATATATAT
1 ATATA-ATATAATATATAT
10760 A
1 A
10761 AGAGAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAATATAATATATAT
Found at i:12240 original size:11 final size:11
Alignment explanation
Indices: 12216--12250 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12206 TTGACAGCGT
12216 AACAAAAACAA
1 AACAAAAACAA
* *
12227 AACGAAAACGA
1 AACAAAAACAA
12238 AACAAAAACAA
1 AACAAAAACAA
12249 AA
1 AA
12251 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Done.